Identification of Potential Gene Interactions in Heart Failure Caused by Idiopathic Dilated Cardiomyopathy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30368515", "kind": "science-record", "revision": 9, "content_hash": "sha256:bbabfd13a6c5eebf323b104f98140c8b548d39ef9e5d040f45b60e445d982a74", "created_at": "2026-11-01T15:40:38Z", "updated_at": "2026-11-01T22:43:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Potential Gene Interactions in Heart Failure Caused by Idiopathic Dilated Cardiomyopathy.", "doi": "10.12659/MSM.912984", "pmid": "30368515", "authors": ["Huijuan Huang", "Beibei Luo", "Boqun Wang", "Qianwen Wu", "Yuming Liang", "Yan He"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2018, "abstract": "BACKGROUND Many heart failure (HF) cases are caused by idiopathic dilated cardiomyopathy (iDCM). This study explored the mechanisms of the development and progression of HF caused by iDCM. MATERIAL AND METHODS The gene expression profiles of 102 samples were downloaded from the GEO database (GSE5406). Differentially expressed genes (DEGs) were identified through GO analysis and a KEGG pathway analysis, respectively. A protein-protein interaction (PPI) network was constructed and analyzed to screen potential regulatory proteins. In addition, MCODE and a cytoHubba plugin were used to identify the module and hub genes of DEGs. Finally, transcription factors (TFs) were predicted using PASTAA. We did not perform whole-exome sequencing (WES) for detecting mitochondrial DNA (mtDNA). RESULTS A total of 197 DEGs were screened, and 3 modules, and 4 upregulated and 11 downregulated hub genes were screened. The GO analysis focused on the terms and 12 KEGG pathways were enriched. The FOS, TIMP1, and SERPINE1 hub genes, as well as some key TFs, demonstrated important roles in the progression of HF caused by iDCM. CEBPD, CEBOB, CDC37L1, and SRGN may be new targets for HF in iDCM patients. CONCLUSIONS The identified DEGs and their enriched pathways provide references for exploring the mechanisms of the development and progression of HF patients with iDCM. Moreover, modules, hub genes, and TFs may be useful in the treatment and diagnosis of HF patients with iDCM. However, mtDNA was not investigated.", "claims": [{"id": "claim-method", "statement": "A Linear Models for Microarray Data (LIMMA) package of R was used to identify the DEGs in the iDCM-HF samples compared with the normal LV samples [12].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30368515", "locator": "sections[5] \"Identification of DEGs\" paragraph 2", "quote": "A Linear Models for Microarray Data (LIMMA) package of R was used to identify the DEGs in the iDCM-HF samples compared with the normal LV samples [12]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression profile of GSE5406 was downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) using the platform GPL96 ([HG-U133A] Affymetrix Human Genome U133A Array; Affymetrix, Inc., Santa Clara, CA, USA). A total of 102 individuals were analyzed in this study. RNA samples for this dataset were extracted from explanted left ventricular (LV) myocardia of 86 patients with systolic HF due to iDCM (iDCM-HF), and 16 unused donor hearts with normal LV functions at the time of harvest were used as controls [9].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30368515", "locator": "sections[3] \"Data source\" paragraph 2", "quote": "The gene expression profile of GSE5406 was downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) using the platform GPL96 ([HG-U133A] Affymetrix Human Genome U133A Array; Affymetrix, Inc., Santa Clara, CA, USA). A total of 102 individuals were analyzed in this study. RNA samples for this dataset were extracted from explanted left ventricular (LV) myocardia of 86 patients with systolic HF due to iDCM (iDCM-HF), and 16 unused donor hearts with normal LV functions at the time of harvest were used as controls [9]."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:30368515"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE5406"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE5406"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30368515", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/MSM.912984", "sha256": "sha256:8a14dafe0d4bacf8a2d009bd02aaad4920db5a62e0b1992e96d35db032999279", "bytes": 31527, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12659/MSM.912984", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6216482", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE5406", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5406", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE5406", "version": null, "note": "The gene expression profile of GSE5406 was downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) using the platform GPL96 ([HG-U133A] Affymetrix Human Genome U133A Array; Affymetrix, Inc., Santa Clara, CA, USA). A total of 102 individuals were analyzed in this study. RNA samples for this dataset were extracted from explanted left ventricular (LV) myocardia of 86 patients with systolic HF due to iDCM (iDCM-HF), and 16 unused donor hearts with normal LV functions at the time of harvest were used as controls [9].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression profile of GSE5406 was downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) using the platform GPL96 ([HG-U133A] Affymetrix Human Genome U133A Array; Affymetrix, Inc., Santa Clara, CA, USA). A total of 102 individuals were analyzed in this study. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE5406"], "resolved_accessions": ["GSE5406"], "statements": ["The gene expression profile of GSE5406 was downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) using the platform GPL96 ([HG-U133A] Affymetrix Human Genome U133A Array; Affymetrix, Inc., Santa Clara, CA, USA). A total of 102 individuals were analyzed in this study. RNA samples for this dataset were extracted from explanted left ventricular (LV) myocardia of 86 patients with systolic HF due to iDCM (iDCM-HF), and 16 unused donor hearts with normal LV functions at the time of harvest were used as controls [9]."], "basis": "The paper names GSE5406 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:30368515", "data:geo:GSE5406", "asset:table:pmid:30368515:1", "asset:table:pmid:30368515:2", "asset:table:pmid:30368515:3", "asset:table:pmid:30368515:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE5406"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:12:39Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 26942, "completion_tokens": 1123, "cached_tokens": 640}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:30368515", "type": "paper", "label": "pmid:30368515"}, {"id": "source:pmid:30368515", "type": "manuscript", "label": "PMID 30368515 full text"}, {"id": "data:geo:GSE5406", "type": "dataset", "label": "GEO GSE5406"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30368515", "type": "paper", "label": "pmid:30368515"}, {"id": "source:pmid:30368515", "type": "manuscript", "label": "PMID 30368515 full text"}, {"id": "data:geo:GSE5406", "type": "dataset", "label": "GEO GSE5406"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30368515", "type": "extraction", "used": ["source:pmid:30368515"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE5406", "type": "accession_resolution", "used": ["data:geo:GSE5406"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:30368515", "parent_hash": "sha256:14fd75a1ea89852893cdc47f530c034988361da10af74d414ce07f5fdbd78a03", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE5406 licence not read", "asset:data:geo:GSE5406 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["A Linear Models for Microarray Data (LIMMA) package of R was used to identify the DEGs in the iDCM-HF samples compared with the normal LV samples [12]."], "order_basis": "analysis_only", "id": "assay:1"}]}